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Add a parameter for lab differentials converted to absolute values

Source: R/derive_param_wbc_abs.R
derive_param_wbc_abs.Rd

Add a parameter by converting lab differentials from fraction or percentage to absolute values

Usage

derive_param_wbc_abs(
  dataset,
  by_vars,
  set_values_to,
  get_unit_expr,
  wbc_unit = "10^9/L",
  wbc_code = "WBC",
  diff_code,
  diff_type = "fraction"
)

Arguments

dataset

Input dataset

The variables specified by the by_vars argument are expected to be in the dataset. PARAMCD, and AVAL are expected as well.

The variable specified by by_vars and PARAMCD must be a unique key of the input dataset, and to the parameters specified by wbc_code and diff_code.

by_vars

Grouping variables

Permitted Values: list of variables created by exprs() e.g. exprs(USUBJID, VISIT)

set_values_to

Variables to set

A named list returned by exprs() defining the variables to be set for the new parameter, e.g. exprs(PARAMCD = "LYMPH", PARAM = "Lymphocytes Abs (10^9/L)") is expected.

get_unit_expr

An expression providing the unit of the parameter

The result is used to check the units of the input parameters.

Permitted Values: a variable containing unit from the input dataset, or a function call, for example, get_unit_expr = extract_unit(PARAM).

wbc_unit

A string containing the required unit of the WBC parameter

Default: "10^9/L"

wbc_code

White Blood Cell (WBC) parameter

The observations where PARAMCD equals the specified value are considered as the WBC absolute results to use for converting the differentials.

Default: "WBC"

Permitted Values: character value

diff_code

white blood differential parameter

The observations where PARAMCD equals the specified value are considered as the white blood differential lab results in fraction or percentage value to be converted into absolute value.

diff_type

A string specifying the type of differential

Permitted Values: "percent", "fraction" Default: fraction

Value

The input dataset with the new parameter added

Details

If diff_type is "percent", the analysis value of the new parameter is derived as $$\frac{White Blood Cell Count * Percentage Value}{100}$$

If diff_type is "fraction", the analysis value of the new parameter is derived as $$White Blood Cell Count * Fraction Value$$

New records are created for each group of records (grouped by by_vars) if 1) the white blood cell component in absolute value is not already available from the input dataset, and 2) the white blood cell absolute value (identified by wbc_code) and the white blood cell differential (identified by diff_code) are both present.

See also

BDS-Findings Functions for adding Parameters/Records: default_qtc_paramcd(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_locf_records(), derive_param_bmi(), derive_param_bsa(), derive_param_computed(), derive_param_doseint(), derive_param_exist_flag(), derive_param_exposure(), derive_param_framingham(), derive_param_map(), derive_param_qtc(), derive_param_rr(), derive_summary_records()

Examples

library(tibble)

test_lb <- tribble(
  ~USUBJID, ~PARAMCD, ~AVAL, ~PARAM, ~VISIT,
  "P01", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
  "P01", "WBC", 38, "Leukocyte Count (10^9/L)", "CYCLE 2 DAY 1",
  "P01", "LYMLE", 0.90, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1",
  "P01", "LYMLE", 0.70, "Lymphocytes (fraction of 1)", "CYCLE 2 DAY 1",
  "P01", "ALB", 36, "Albumin (g/dL)", "CYCLE 2 DAY 1",
  "P02", "WBC", 33, "Leukocyte Count (10^9/L)", "CYCLE 1 DAY 1",
  "P02", "LYMPH", 29, "Lymphocytes Abs (10^9/L)", "CYCLE 1 DAY 1",
  "P02", "LYMLE", 0.87, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1",
  "P03", "LYMLE", 0.89, "Lymphocytes (fraction of 1)", "CYCLE 1 DAY 1"
)

derive_param_wbc_abs(
  dataset = test_lb,
  by_vars = exprs(USUBJID, VISIT),
  set_values_to = exprs(
    PARAMCD = "LYMPH",
    PARAM = "Lymphocytes Abs (10^9/L)",
    DTYPE = "CALCULATION"
  ),
  get_unit_expr = extract_unit(PARAM),
  wbc_code = "WBC",
  diff_code = "LYMLE",
  diff_type = "fraction"
)
#> # A tibble: 11 × 6
#>    USUBJID PARAMCD  AVAL PARAM                       VISIT         DTYPE      
#>    <chr>   <chr>   <dbl> <chr>                       <chr>         <chr>      
#>  1 P01     WBC     33    Leukocyte Count (10^9/L)    CYCLE 1 DAY 1 NA         
#>  2 P01     WBC     38    Leukocyte Count (10^9/L)    CYCLE 2 DAY 1 NA         
#>  3 P01     LYMLE    0.9  Lymphocytes (fraction of 1) CYCLE 1 DAY 1 NA         
#>  4 P01     LYMLE    0.7  Lymphocytes (fraction of 1) CYCLE 2 DAY 1 NA         
#>  5 P01     ALB     36    Albumin (g/dL)              CYCLE 2 DAY 1 NA         
#>  6 P02     WBC     33    Leukocyte Count (10^9/L)    CYCLE 1 DAY 1 NA         
#>  7 P02     LYMPH   29    Lymphocytes Abs (10^9/L)    CYCLE 1 DAY 1 NA         
#>  8 P02     LYMLE    0.87 Lymphocytes (fraction of 1) CYCLE 1 DAY 1 NA         
#>  9 P03     LYMLE    0.89 Lymphocytes (fraction of 1) CYCLE 1 DAY 1 NA         
#> 10 P01     LYMPH   29.7  Lymphocytes Abs (10^9/L)    CYCLE 1 DAY 1 CALCULATION
#> 11 P01     LYMPH   26.6  Lymphocytes Abs (10^9/L)    CYCLE 2 DAY 1 CALCULATION